Well, in D&D, as well as any other TTRPG I’ve played, players don’t have to roll for obviously trivial tasks like pushing a door open or saying something.
So flapping arms wouldn’t need a skill check.

But yes, in D&D, only the natural 20 and sometimes natural 1 are relevant, so we can talk about them by adding the word “natural” in front of them.
In any other case, the end result including the modifiers matters, so when we say we roll a certain number like 18, we mean after adding in any relevant modifiers.